Storing InterProScan results in CHADO

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Storing InterProScan results in CHADO

Cornel Ghiban
Hi,

Is there a way to add properties to a feature property?

Here's what I'd like to do, perhaps it's wrong:

Given a feature (gene usually), I'd like to get all the data from
InterPro(Scan) based on the translated sequence of that feature, and store it
in chado. And the results from InterPro have certaing properties, like GO
terms, abstracts, etc.

Or maybe  I should ask this: Is there a way of storing functional annotation
(InterproScan results) for a feature, in chado?

Thanks,
Cornel Ghiban


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Re: Storing InterProScan results in CHADO

Don Gilbert-2-3

Cornel,

You could use feature properties, but what you have is an analysis,
like Blast, etc., where your gene proteins match InterPro database
entries with some score, ie. some uncertainty.  So the Chado way
would be to store these as analysisfeatures.
This page shows a worked example for Blast analysis,
http://gmod.org/wiki/Load_BLAST_Into_Chado

I don't know if there is a simple example or software for loading
Interpro analyses, but there is such in the more extensive Drupal (php)
project called Tripal, see
http://gmod.org/wiki/GMOD_News#Tripal_v0.2_Released

You may want to view the Tripal code, esp. tripal_analysis_interpro.module
   tripal_analysis_interpro_parseHTMLFile = load interpro analysis to chado
   tripal_get_interpro_results = view chado results

to see how they store Interpro data into Chado tables.  Generally GO, etc.
database info is stored as separate DB information, then linked via
analysisfeatures by database IDs to your gene features.  That way you can
update the GO, Interpro, etc. public DB data separately, or link many
genes w/ same function to single GO db entries.

- Don Gilbert
-- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405
-- [hidden email]--http://marmot.bio.indiana.edu/

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Re: Storing InterProScan results in CHADO

Stephen Ficklin
In reply to this post by Cornel Ghiban
Hi Cornel,

We wanted to do a similar thing.  We ended up creating an analysisfeatureprop table, which I believe got incorporated into the new release of chado, or at least we had a discussion about including it.  I haven't tried the new release yet.  

We store a record for the InterProScan analysis in the analysis table, and then use the analysisfeature table to associate which features were involved in the analysis and then use the analysifeatureprop table to store the InterProScan results for each feature.  

Hope that helps.

Stephen

-----Original Message-----
From: Cornel Ghiban [mailto:[hidden email]]
Sent: Saturday, July 17, 2010 12:44 PM
To: [hidden email]
Subject: [Gmod-schema] Storing InterProScan results in CHADO

Hi,

Is there a way to add properties to a feature property?

Here's what I'd like to do, perhaps it's wrong:

Given a feature (gene usually), I'd like to get all the data from
InterPro(Scan) based on the translated sequence of that feature, and store it
in chado. And the results from InterPro have certaing properties, like GO
terms, abstracts, etc.

Or maybe  I should ask this: Is there a way of storing functional annotation
(InterproScan results) for a feature, in chado?

Thanks,
Cornel Ghiban


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